I see that we can right click on an object and select the 'Script object as ALTER' option to script individual objects. Is there anyway to use this option (or any other option with SQL Prompt) to script out multiple objects at once?

I want to script out multiple encrypted stored procedures all at the same time. I can do this for unencrypted procedures using the method you mentioned. But the 'Script Objects as ALTER' option provided by SQL Prompt is not available from the object explorer details window. And that is the only option I can use to script encrypted objects.

Unfortunately I don't think there's an easy way to get to this in Prompt at the moment (although annoyingly we do already have the code in place since you can script multiple invalid objects in the "Find Invalid Objects" page). We do have a related uservoice request for scripting things from the object explorer so please add your vote to it.

In the meantime you could use SQL Compare to create a scripts folder from your database then navigate to the folder and copy the scripts out. A guide for how to do so can be found here.